Posted
by
samzenpus
on Monday May 13, 2013 @01:01PM
from the who-needs-it? dept.

sciencehabit writes "The carnivorous humped bladderwort, found on all continents except Antarctica, is a model of ruthless genetic efficiency. Only 3% of this aquatic plant's DNA is not part of a known gene, new research shows. In contrast, only 2% of human DNA is part of a gene. The bladderwort, named for its water-filled bladders that suck in unsuspecting prey, is a relative of the tomato. The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life."

This demonstrates only that organisms with little junk DNA can exist. To really demonstrate that "junk DNA" does nothing, someone needs to take an organism that has lots of junk DNA, sequence it, replace all the junk with the DNA equivalent of nulls, synthesize the new DNA, grow a new organism, and produce a few generations of it. Good project for Craig Venter.

There's a suspicion that "junk DNA", while currently turned off, sometimes gets turned on when mutation flips a bit, and this helps evolution along. An organism with little or no junk DNA may not evolve further, but can exist and reproduce just fine.

I believe a more prudent falsifiable hypothesis would run along the lines of (and I'm sorry, I'm only a software developer): Due to relaxed external selective pressures the bladderwort's RNA polymerase has become adept at writing coding errors to the 3% noncoded DNA during replication and this actually still serves a vital function -- especially if the bladderwort is to survive in a much larger window than a few generations.

As a biologist and software developer, I have a hard time understanding what you are trying to say here.

Um, where do you get those numbers? At least 76% of the non-coding human genome is transcribed [sciencemag.org] -- to what end we cannot be certain in all cases, but the RNA transcripts from these often are fed back into gene expression and regulation. It's estimated that well over 50% of non-coding DNA is heavily conserved by evolutionary processes and contributes significantly to fitness.

Junk for an individual. Not necessarily junk for the evolution of a species. This issue comes up in computer science too with genetic algorithms, pushing pressure to keep the encoding as compact as possible 'may' lead to the side effect of increasing the probability of being stuck on a local optima. There's a lot of math 'n stuff involved that can better be explained by experts, but here's the short version: let's say that a genetic algorithm engine has an individual settled for a local optimum with all the bits just right. But there's a possible mutation that could lead to finding a slope leading to a better optimum. Obviously there's the issue that the mutation is going to compromise something important, and you end up with a mutant with good potential but a weaker fitness score, so the mutation is more likely to be discarded. However, if there's non-functional bits in the individual, there's a higher chance that the mutant can score better by compromising something that wasn't in use to being with, hence non-functional coding genes having some use in the long run. Now this is a huge simplification on a complex matter, but this does come up.

I note that the little digital clock on my desk does not need a 1TB disk drive full of software in order to operate either.

Constructing a large mammalian brain complete with things like "instincts" might well make use of non-protein-coding information of some sort.

One thing about biology and the functioning of cells that you learn pretty quick is that "if it can happen then it probably does", and this is a very strong argument against writing off anything that appears to be conserved as "useless".

Simply finding an organism that itself has no need of other information simply says that it's not a universal requirement, and doesn't really tell you anything about whether other organisms might have found a use for it.

If you have a big enough ego, everything you don't understand must be unimportant junk.

I think people read too much into the use of the word "junk", and attribute a pejorative meaning that wasn't necessarily intended. The best explanation I've seen (can't remember the source, sorry) was something along the lines of "junk is the stuff I keep in my attic; stuff I throw out is garbage." Biologists are in fact aware that non-coding parts of the genome can be essential, and there was never any presumption that anything we didn't understand was unimportant - however, how much of the non-coding DNA is genuinely necessary is an open question, and it's hard to find an obvious use for most of it. Clearly some complex organisms get along fine without it, so it's not unreasonable to view junk DNA primarily as a side effect of millions of years of evolution.